I was working on one of the new GD55 p67 boards from MSI, when there was a failed BIOS flash. After clearing the CMOS, the system presented us with options to enter Setup or Continue. Unfortunately, hitting the related keys, F1 and F2 respectively, does nothing.

Can't tell if it's not reading the keyboard(though the numlock light is on), or if it's accepting the command and doing nothing.

This happens sometimes. PS/2 connected keyboards tend to work better at this point, but generally, a wired keyboard will be detected, and should be able to allow you to press the keys, and have them recognised.
You didn't mention, but did you try only having the keyboard, power, and monitor connected? Might increase chances of it recognising input.

Unfortunately nothing has succeeded so far, despite both suggestions given seem very logical and got hopes up!

Trying the os/2 port is fine, in the sense that the Keyboard flashes it's lights, but still doesn't work. I wonder if it has to do with the fact that the ps/2 port is for mouse OR keyboard. When the system reboots, it lists the connected peripherals. 1 KBD, 1 MICE, 0 MASS, 0 etcetc

But there is no mouse connected.

Function would be fine, but A) keyboard doesn't have it B) It worked before the flash.

And ya, we just have the VGA, one stick of RAM, CPU+Fan, and keyboard connected.
We can't test without the RAM as it won't even attempt to POST or give failure beeps - it simply shuts off.